


Ghost in the Machine

by orphan_account



Series: Zemblanity [1]
Category: Star Trek: Alternate Original Series (Movies)
Genre: Ghosts, Horror AU, M/M, Supernatural Elements, WIP, creature feature, things that go bump in the night - Freeform
Language: English
Status: Completed
Published: 2013-08-05
Updated: 2013-08-05
Packaged: 2017-12-22 13:42:34
Rating: Mature
Warnings: Graphic Depictions Of Violence
Chapters: 2
Words: 3,409
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/913865
Author URL: https://archiveofourown.org/users/orphan_account/pseuds/orphan_account
Summary: <blockquote class="userstuff">
              <p>“’Let the spirit out’, Bones? That’s crazy talk. I mean… do you guys really do that still, back on Earth? Open windows to let people’s ‘ghosts’ out?”</p><p>Jim believes in science. What he can see, smell, touch, taste, hear. But when things start to go downright WEIRD aboard the Enterprise, and the only cause appears to be supernatural, Jim is forced to admit that perhaps there are more sinister things at play.</p>
            </blockquote>





	1. Chapter 1

**Author's Note:**

> So a supernatural horror alternate universe. This is going to have strong horror elements in it, lots of gore, eventual sex and all that good stuff.
> 
> This prologue actually sets up the overall plot of the series, something that won't be resolved for a while because I'm cruel. Another chapter will be posted soon (tonight or tomorrow).

“Get off my fucking bridge right now!” Jim shouted, rising from his chair and drawing his phaser. He kept it steadily pointed at the pair who had sauntered onto his bridge like they owned it. He could see his bridge crew shifting in their seats, assessing the threat themselves, reaching for weapons or adjusting their feet ready to dive for cover should a fire fight break out.

“I’m afraid, Captain, that you do not have the power to remove us from this bridge, or the ship for that matter, until we have got what we came for,” the Agent said. His eyes were a cold, unfeeling grey. His leather uniform creaked as he stepped forward, unconcerned by the phasers pointed in his direction.

“Identify yourself before I take you out as a threat to my ship,” Jim turned his voice cold. He was stalling for time, hoping to any higher being that would listen that Nyota had got the message out to Sickbay somehow, anyhow, that they were under attack.

“My name is Agent Smith, and this is my colleague-“

“Let me guess, his name is Smith too?” Jim bit out sarcastically. Agent Smith’s eyes crinkled but his lips didn’t so much as twitch.

“Jones, actually. Seems you might know why we’re here, Captain. So let’s make a deal. Give us what we want, and we will go away,” he said, holding his hands out as though it were the simplest thing in the world.

Like Jim could just give over _Bones_ like that.

“I don’t know what you want. I assure you, my ship doesn’t need Section 31 messing with it again,” he said, staring the Agent down. This time the Agent did laugh, a hollow, eerie sound that made all the hairs on the back of Jim’s neck stand on end.

“We are taking Doctor McCoy, Captain. In fact…” The Agent put a hand to his ear as though listening to rapturous applause. “Ah, yes, we already have him. They scream so well when you do that to them…”

Jim swallowed around the lump in his throat, trying to keep his hand steady and his face impassive and failing.

“Do what to him?” he asked, refusing to refer to Bones as anything other than the human being he was. Goddamn it, how inhuman _were_ these people?

The Agent smiled, white, white teeth flashing.

“Why, burn him of course.”


	2. 9 Months Earlier...

**Summary for the Chapter:**

> “Maybe you did? Wouldn’t be the first time there were mass hallucinations aboard the Enterprise,” Bones pointed out, sipping his beer. Jim tried not to pay attention to the way Bones’ throat moved as he swallowed.

**Notes for the Chapter:**

> Whew, got this finished so though I'd get it up!

“We’re losing her!”

“Damnit! Chapel-”

“Already on it McCoy!”

“Heart rate still decreasing-“

Jim craned his head from his own rest bed to see what the doctors were doing. A screen had been hastily drawn around the biobed but there was a gap where Jim could see the back of Bones’ back. He could hear the hastily shouted command, the erratic beeping of the machines.

There was the sound of a flatline and Jim let his head drop back to his pillow. Goddamnit. That made four. Four this mission, lost to a stupid _trade dispute_.

“Time of death 16:52,” Bones said heavily and the screens were drawn back. The Ensign’s face was already covered and Jim clenched his fist, trying not to cast his mind back to the start of the mission. She’d been bright, vibrant, excited about the opportunity to make contact with a new race of people.

“I’ll take care of her, Doctor,” Chapel said, patting Bones on the back. The rest of the medical team dispersed and Chapel wheeled the biobed out of the room. Jim watched them all. Bones went to his office almost immediately, but the others dithered and dallied, checking up on other patients. Their behaviour was strange, almost… jumpy. Jim expected them to be depressed, but their behaviour didn’t seem to match.

He was puzzling over it when Bones came back out of his office, casting a look over Sickbay before he saw Jim was awake. He walked over, tricorder already at the ready.

“That was Ensign Dobromil, right?” Jim asked. Bones nodded, his gaze focused on the tricorder. Jim knew better than to push. Bones was concentrating on taking his readings and Jim knew he would be told what mattered when the doctor came to a conclusion. He glanced around the Sickbay.

One of the nurses jumped a little too much when someone put their hand on her shoulder. She whirled around and then laughed self-consciously when she realised it was just another crew member.

“Sickbay always this jumpy when you lose someone?” Jim asked. Bones looked up from the tricorder, then over his shoulder at the other biobeds.

“Doctors are superstitious folk,” Bones replied, turning his attention back to the tricorder. “Makes us jumpy when we can’t let the spirit out.”

Jim raised his eyebrows at that. Bones didn’t appear to think he’d said anything weird though. He cleared his throat, forcing those hazel eyes to look up from his tricorder for a moment.

“’Let the spirit out’, Bones? That’s crazy talk,” he said, gesturing around. “I mean… do you guys really do that still, back on Earth? Open windows to let people’s ‘ghosts’ out?”

Bones’ mouth quirked up into a small smile and he dropped the tricorder. “Yeah we do Jim. Now your readings show…”

* * *

 

Getting out of Sickbay was always one of Jim’s top priorities when being injured. Sitting there, listening to other people being ill, it made him uneasy. Bones walked around unaffected by it all, in his element, talking to people with that kind Southern drawl and occasionally casually flirting with the other staff.

But being a patient was different. It was like being an outsider inside his own ship and Jim hated it. In Sickbay there were no ranks, no differences between people, and while Jim enjoyed the _spirit_ of the idea, in practice it left him cranky. He didn’t want people to see him weak or for others to overhear Bones scolding him into _lying back down for God’s sake Jim_.

Luckily, his injuries hadn’t been severe enough to keep him longer than a few more hours after Ensign Dobromil had passed away. Bones had checked him over one last time before inviting him into his office and pouring him a drink.

“Are you going to have to go back onto that goddamn planet?” Bones asked and Jim shrugged, taking the offered bourbon and sitting in the visitor’s chair. He put his feet up on Bones’ desk and ignored the other’s scowl in his direction.

“Depends on if Starfleet thinks what they have is important enough. Personally, I want to get the hell away from this place and into deep space as soon as possible,” he said, taking a sip of the drink. Bones regarded him over the desk for a moment.

“Any chance we can transport Ensign Dobromil’s body off the ship before we leave? Don’t really want to cart her around the galaxy if I can help it Jim,” he said. Jim raised an eyebrow. Usually Bones wouldn’t have asked his permission. They had done numerous space burials during their time aboard the Enterprise and Jim had the casualty list permanently open on his computer, logging each one and what he’d said. That Bones was so adamant about this particular one…

“We can but… why? I mean, a normal space burial should be fine right?” he asked, shrugging slightly. “Or did her parents have specific wishes?”

“Her parents are dead, Jim. It’s not that. It’s just… she died a rather violent death. Her legs were completely ripped off by that blast. I just think it’s best to draw a line under it quickly rather than let it fester. It affects the staff when there’s something in the morgue,” Bones replied, taking a sip of his bourbon and relaxing into his chair. Jim thought about it. Really, he couldn’t think of a reason to protest it, just that it was odd that Bones was suddenly superstitious about something so ridiculous.

“Yeah sure. You’ll have to wait a day or so while Starfleet decides on our orders but sure. Whatever,” he said. Bones’ eyes closed for a moment before he smiled.

“Thank you Jim.”

* * *

 

The conversation was still predominant in Jim’s mind as he walked to the bridge later. He felt heavy, losing an officer was always hard, but the aura in Sickbay had been different. It had been on edge and Jim couldn’t shake the eerie feeling and the urge to glance over his shoulder.

Which was _absurd._

“Captain on the bridge,” Chekov chirped when he entered. Jim nodded to the various crew members who had looked up, silently enquiring about his health. He took his seat and took the PADD Spock offered him.

“I am glad you are recovered quickly, Captain. We have received numerous transmissions from the planet that have required your attention,” Spock said. Jim sighed and gestured to the screen.

“Bring ‘em up. Let’s see the show reel,” he said. The transmissions were all relatively short, all expressing similar sentiments of dismay that the trade agreement had been affected by what the ambassadors assured Starfleet were just a few _dissidents_ and nothing that would affect what had been agreed if Captain Kirk would just be _so kind_ as to risk his life and go back onto the planet to sign on the dotted line.

“Yeah, no,” Jim said, turning in his seat to look at Nyota. “Send a politely worded message back, Lieutenant. Let them know that we’re in orbit awaiting orders and that we aren’t going back down there without Starfleet’s express command to do so.”

Uhura set to work and Jim glanced down at his PADD. As always, his inbox was full of messages of varying degrees of urgency. He never really read _all_ of them, which would probably give Spock apoplexy but he read the ones that were flagged. One of those caught his attention simply because the subject line was so absurd.

[Too Much Blood in Sickbay].

Jim clucked his tongue as he opened it up. It was from one of the Yeoman who worked in the cargo bay. Apparently she had been put in charge of Sickbay’s supplies and was… questioning the amount of blood they were taking aboard at each space station.

_It’s not my place to question the practices of the physicians in Sickbay, nor am I implying foul play on the part of Doctor McCoy, however I do think that it’s important to note that the Enterprise has taken on board enough blood to **give everyone on board a transfusion** over the last year. We are using three times as much blood as any other ship in the ‘fleet. I wished you to be aware that I am monitoring the situation, Captain, and am trying to determine where this blood could possibly be going._

Jim rubbed his face. Obviously he wasn’t giving some of his staff down in the cargo bay enough to do if they were taking down details like this. Who cared if Sickbay was using a bit too much blood? Jim was sure that they were using just enough to keep everyone alive and safe. And stocking too much of the stuff, well, he’d rather be overstocked on something like blood than anything else.

He typed back a flippant response, something along the lines of ‘ _Keep up the good, important work, Yeoman’_ and sent it back, throwing the PADD to one side and staring moodily at the screen in front of him.

He really didn’t want to go back down to that planet.

“Captain! We’re getting odd readings… I can’t decipher quite what it is but… It seems like ships perhaps?” One of the science officers was saying. Jim immediately sat up in his seat. Had the ‘dissidents’ on the planet got spacecraft now? Was the Enterprise going to come under attack from such a primitive spacefaring species? Jim almost felt sorry for them.

Spock made his way to the station where the confused Ensign was staring at the screen. When he got there his eyebrow raised.

“How long have you been on shift, Mr Amando?” he asked. Jim sighed. A false reading, huh? Well, that was just peachy. Now they’d actually have to wait on Starfleet’s orders.

“I swear to you, sir, that reading was there. I don’t understand. Everything was going haywire a minute ago and now-“

“Keptin! We are off course and in danger of entering the atmosphere. Sulu, you must-“

“Captain, picking up white noise transmissions on all frequencies-“

The klaxon started and Jim stared around the bridge. He stood up, walking over to Spock, who was using his own terminal to take readings, his fingers dancing over buttons and touch screens to locate the problem.

“Is it a stealth ship with a scrambler? What are we dealing with Mr Spock?” Jim shouted over the klaxon. Officers were all at battle stations, as though the klaxon had been ordered instead of spontaneously going off. Jim cursed.

“There is nothing outside the Enterprise. In fact the nearest ship is a cruise ship light years away and definitely does not have anything aboard that could be causing our malfunctions,” Spock said. Jim made a noise of frustration, walking back to his chair and hitting the communications button.

“Bridge to Lieutenant Commander Scott,” he said urgently. “Come in Scotty.”

There was a pause and then a horrific sound emitted from the speakers. A screeching sound like a combination of dial-up internet and nails being drawn down a blackboard. It was in that moment, almost as soon as it started, that everything stopped.

Jim sat there, staring blankly around the bridge.

“Aye, Captain, what can I do for yeh?” Scotty’s voice came through the speaker cheerfully. Jim swallowed.

“We’re having malfunctions on the bridge. Send up a team.”

* * *

 

It had been a hard day. Jim stripped off his clothes, stepping into the shower and scrubbing his skin. His hand lingered over the newly regenerated flesh on his shoulder. Bones had patched that up earlier and it still felt sensitive and new. He traced over it with the pads of his fingers, gentler than McCoy’s hands had been. Those had been firm, professional, not the soft caress that Jim had wished for.

He shook his head, water spraying onto the tiles as he tipped his head back. The water stung the new skin a little, but it felt good to just be clean all the same. Jim stood under the spray for as long as he could, until the guilt at using that much water started to eat at him and he turned off the shower with a pout.

He towelled himself off quickly, rubbing at his skin until it was bright and pink, before wrapping the towel around his waist and opening the door to his quarters. He padded across the carpet to where he’d laid out some lounging about clothes, discarding the towel and pulling on the sweat pants and a t-shirt from his graduating class at the academy.

He heard the door go just as he was towelling his hair for the final time. He walked over to the door, pressing the button to let it slide open. Bones was on the other side, a four-pack in one hand and a holovid case in the other.

“Thought you might want something to take your mind off how your own ship appears to be out to get ya,” the doctor said, his mouth quirked into a smirk. Jim rolled his eyes.

“Yeah, yeah. Sure does travel fast when my lady gets her knickers in a twist, doesn’t it?” he replied, taking a step back from the door. Bones hovered awkwardly in the corridor.

“Come in, Bones! Geez,” Jim said, gesturing for the other to come in. Bones stepped in and made his way to his spot on Jim’s couch. Before long they were both into their second beer and discussing at length what had gone wrong so far with this mission.

Usually, Jim was much more positive than his CMO about how a mission had gone, but tonight he couldn’t see how anything had gone particularly well. The Enterprise clearly had thrown a tantrum earlier, one that could have had devastating consequences if they were in battle or during an emergency. And Scotty couldn’t figure out anything about it. He couldn’t even find copies of the data involved.

He had actually asked them if they had _dreamed_ it.

“Maybe you did? Wouldn’t be the first time there were mass hallucinations aboard the Enterprise,” Bones pointed out, sipping his beer. Jim tried not to pay attention to the way Bones’ throat moved as he swallowed.

“It didn’t feel like that, Bones. Something honestly was sending those things haywire… I just don’t know what it was yet. Chekov’s spending his evening trying to get the black box data to see if our systems have been tampered with,” Jim replied, sagging back against the couch. He refused to think it was just a glitch or that it had been the result of their joint perceptions acting against them. It had felt too real to have all been fake and it would mean psychological testing for nearly every experienced member of his bridge crew.

“Well, enough work, Jim. We’re off duty. Let’s just watch a bad movie and pretend we’re not in space for an hour or so,” Bones said, huffing as he got off the sofa. Jim couldn’t help but smile at the grouching, watching as Bones made his way to the holovid player and pushed the buttons to operate it like a gorilla. He knew that Bones had grace and elegance, that those hands were steadier than a beating drum, but sometimes Bones acted like a complete Neanderthal. Especially around technology.

“Stop being a luddite and be gentle with it,” Jim scolded playfully. Bones looked over his shoulder, eyebrow raised, and then hit the button to play the thing with undue force. Jim laughed and shifted a little when Bones returned to the couch.

They were barely two feet apart and yet it felt like the world. Jim was always aware of the distance between them, how near or close. It was almost like he had a sixth sense that told him where Bones was at all times in direct relation to himself. Sometimes it was so close it set his skin on fire, others it was far enough away for him to feel a cool worry. Now, it felt familiar and warm, like a thousand times before.

A thousand times when Jim had pushed that warmth away rather than basked in it and firmly drawn the line.

Friend.

Best friend.

Off-limits.

They watched the film with their own dry commentary over the top. Half way through, the beers were finished and Jim took the empties to the chute. Upon returning he found Bones grumbling to himself about how the leading male looked like he’d been bandaged up by a barber causing Jim to laugh and ask the other to point out all the other medical inaccuracies in the scene.

In one particularly fine rant about the monitors at the hero’s bed side, Jim’s communicator chirped. He flipped it open and Bones went silent immediately, pausing the film.

“Kirk,” he said calmly. There was static for a few moments then-

“Chekov here, Keptin. You told me that I should tell you if I am finding anything and I am finding lots of things that back up our story over Scotty’s,” Chekov reported. Jim raised his eyebrows at Bones in an ‘I told you so’ gesture. Bones shrugged, looking amused.

“It is odd though. The information… It is not being hard to get to, just hidden wery well,” Chekov continued. “And it is… Wait, Keptin… It is changing… I cannot read it anymore. It has become gibberish.”

Jim scowled. “Did you download it already, Chekov?”

“Keptin! I am losing power in my quarters! Ship lights are not supposed to flicker?”

Jim got to his feet. Bones followed him immediately. He stooped to put his boots on, the static from the communicator becoming deafening.

“This is most strange! Sir! I am-“

Whatever Chekov was, Jim didn’t find out because at that moment the Ensign’s scream distorted the transmission. Jim looked up at Bones, alarmed. The doctor was already dashing for the door though, hitting the button to open it without glancing back to see if Jim was following him.

“ _Prizrak! Keptin, eto prizrak!”_

The communicator went dead in Jim’s hand.


End file.
